Transcript Topic 1 Introduction to Classification and Phylogenetics

Tree of Life
 Planet
Earth is about 4.6 billion years old.
 Oldest known rocks are about 3.8 billion
years old.
 Oldest fossils (prokaryotes) are about 3.5
billion years old.
Tree of Life
 All
living organisms on this planet share a
common ancestor.

The tree of life reflects the branching
pattern of speciation (phylogenetic history
of life) that has occurred since the origin of
life.
Tree of Life
 There
is an excellent Tree of Life website
in which you can trace the branching
pattern of the history of life and explore
classification.
 http://tolweb.org/tree/
Tree of Life
 There
is a hierarchichal classification of
life in which organisms are progressively
nested within larger and larger categories
as more distant relatives are included in
the classification (we will explore
classification shortly).
 The highest level of classification is the
Domain of which there are three.
26.22
“Bacterial” Domains
 Domain
Bacteria
 Domain Archaea
 The
domains Bacteria and Archaea are
both prokaryotes (they have no nucleus
and the DNA is not arranged in
chromosomes). Prokaryote derived from
the Greek Pro meaning before and karyon
meaning a kernel [i.e. a nucleus]
Domain Bacteria
 Bacteria
play a major role in
decomposition and many live symbiotically
with other organisms including humans
helping to break down or synthesize foods
needed by the host.
Domain Bacteria
 Includes
most of the bacteria people are
familiar with including disease-causing
species (Salmonella; Vibrio cholerae
which causes cholera), nitrogen-fixing
(Nitrosomonas) and parasites (Borrelia
burgdorferi which causes Lyme disease).
Domain Archaea

The Archaea include many extremophiles,
organisms that live in extreme environments.

Includes thermophiles which tolerate extreme
heat (e.g. live in geysers and hot springs where
temps may reach 90 degrees celsius) and
halophiles (salt lovers, which live in very saline
environments (e.g. Great Salt Lake, Dead Sea)
Archaea in hot springs
Bacteria and Archaea
 Bacteria
and Archaea are both
prokaryotes and their DNA is arranged in
circular structures called plasmids.
 However, they have substantial
differences in their biochemistry, cell wall
structure and other molecular details.
Domain Eukarya
 Domain
Eukarya contains the eukaryotic
organisms (from Greek eu true and karyon
a kernal) which have a true nucleus and
DNA arranged in chromosomes.
 Eukaryotic
cells are much larger and
complex than prokaryotic cells and contain
organelles such as mitochondria,
chloroplasts, and lysosomes.
Domain Eukarya
 Domain
Eukarya includes three kingdoms
the Plantae, Fungi and Animalia.
 There
are also a number of unicellular
eukaryotes that may form as many as five
other kingdoms. These were formerly
grouped in the paraphyletic group the
Protista.
Domain Eukarya
 Plantae,
Fungi and Animalia are mostly
multicellular, but plants are autotrophic
(produce their own food by
photosynthesis) whereas the fungi and
animals are heterotrophic (consume other
organisms).
Animalia
 Zoology
is the study of animals and
multicellular organisms of the kingdom
Animalia are the focus of this semester,
although we will briefly discuss some
single-celled protozoans (“Protistans”
when discussing a variety of parasitic
diseases).
Animalia

Traditionally, zoologists divide the Animalia into
vertebrates and invertebrates.
 Vertebrates are those that possess a vertebral
column and a suite of other unique derived
features.
 Vertebrates are a subphylum of the phylum
Chordata.
 The Chordata includes all the vertebrates: fish
and tetrapods (amphibians, reptiles, birds and
mammals) and two non-vertebrate chordates the
Urochordates (sea squirts) and the
Cephalochordates (lancelets).
Animalia: Invertebrates

The non-chordate animals are the traditional
Invertebrates and include all the other phyla in
the Animalia. These are the groups we will
focus on this semester.

Major phyla include the Porifera (sponges),
Annelida (earthworms and relatives), Mollusca
(molluscs), Arthropoda (crustaceans, insects
and relatives) and Echinodermata (seastars and
relatives).
Animalia

Animals are heterotrophic eukaryotes. Most are
multicellular.

Except for sponges, all animals have tissues
which are specialized collections of cells that
work together to carry out tasks and are
separated from other tissues by membranes.

Tissues are arranged together to produce
organs and organs are organized into organ
systems (e.g. digestive system).
Animalia
 Most
animals are bilaterally symmetrical
and form a large clade called the Bilateria.
 Bilateral
animals have a left and right side,
top and bottom, as well as front and rear
ends.
A
smaller number are radially symmetrical
(e.g. jellyfish).
Classification
 Before
exploring the many groups of
invertebrate animals we need to review
the general topic of classification or how
we group organisms into a manageable
framework.
Classification
 Science
of Systematics dates to Linnaeus
in the 18th century who devised the basic
systems of binomial nomenclature and
hierarchical classification in use today.
 All
organisms have a unique binomial (2
name) name
 E.g. Humans are Homo sapiens
Classification
 Organisms
are classified into a
hierarchical classification that groups
closely related organisms and
progressively includes more and more
organisms.
Phylogenetic trees
 Systematists
aim to figure out the
evolutionary relationships among
species.
 Branching
diagrams called phylogenetic
trees summarize the evolutionary
relationships among organisms.
Phylogenetic trees
 In
a phylogenetic tree the tips of the
branches specify particular species and
the branching points represent their
common ancestors.
Common ancestor of wolf
and domestic dog
Common ancestor of wolf,
domestic dog, otter and
skunk
Phylogenetic trees
 Phylogenetic
trees are constructed by
studying features of organisms formally
called characters.
 Characters
may be morphological or
molecular.
 Character
similarity resulting from shared
ancestry is called homology.
Cladistics and the construction
of phylogenetic trees
 Cladograms
are diagrams that display
patterns of shared characteristics.
 If
shared characteristics are due to
common ancestry (i.e., they are
homologous) the cladogram forms the
basis of a phylogenetic tree.
Cladograms
 Within
a tree a clade is defined as a group
that includes an ancestral species and all
of its descendants.
 Cladistics
is the science of how species
may be grouped into clades.
Shared derived characters

Cladograms are largely constructed using
synapomorphies or shared derived
characters.

These are characteristics that are evolutionary
novelties or new developments that are unique
to a particular clade.

For example, for birds possession of feathers is
a shared derived character and for arthropods
possession of a jointed limbs and an
exoskeleton are.
Shared primitive characters

Shared primitive characters are characters that
are shared beyond the taxon we are interested
in. Among groups of vertebrates the backbone
is an example because it evolved in the ancestor
of all vertebrates.

If you go back far enough in time a shared
primitive character will become a shared derived
character. Thus, the backbone is a shared
derived character that distinguishes vertebrates
from all other animals.
Constructing a cladogram
 Outgroup
comparison is used to begin
building a cladogram.
 An
outgroup is a close relative of the
members of the ingroup (the various
species being studied) that provides a
basis for comparison with the others.
Constructing a cladogram
 The
outgroup lets us know if a character
state within the ingroup is ancestral or not.
 If
the outgroup and some of the ingroup
possess a character state then that
character state is considered ancestral.
Constructing a cladogram

For example, birds, mammals and reptiles are
all amniotes (produce hard-shelled or amniotic
eggs). Birds have no teeth, but mammals and
reptiles do.

An outgroup to the amniotes, fish, possesses
teeth. Therefore, the ancestral state among the
amniotes is to possess teeth and birds have
secondarily lost them.
Constructing a cladogram
 Having
the outgroup for comparison
enables researchers to focus on those
characters derived after the separation
from the outgroup to figure out
relationships among species in the
ingroup.
Constructing a cladogram
 Cladogram
of various vertebrates:
monkey, horse, lizard, bass and
amphioxus.
 Use
amphioxus as outgroup (is a
chordate, but has no backbone).
Cladogram
Constructing a cladogram

In the cladogram new characters are marked on
the tree where they originate and these
characters are possessed by all subsequent
groups.
Cladograms and Phylogenetic
Trees

A cladogram and a phylogenetic tree are similar,
but not identical.
A phylogentic tree’s branches represent real
evolutionary lineages and branch lengths
represent time or amounts of evolutionary
change.
 Cladogram branches contain no such
information. Branching order of cladogram
should, however, match that of phylogenetic
tree.

Early phylogenetic tree of
amniotes based on
cytochrome c gene by
Fitch and Margoliash (1967).
Note numbers on branches.
These represent estimated
numbers of mutational
changes in gene.
Theories of taxonomy
There are two current major theories of
taxonomy:


Traditional Evolutionary Taxonomy
Phylogenetic Systematics (Cladistics)
 Both
based on evolutionary principles, but
differ in the application of those principles
to formulate taxonomic groups.
Theories of taxonomy
 There
are three different ways a taxon
may be related to a phylogentic tree.
 The taxon may be a monophyletic,
paraphyletic or polyphyletic grouping
Monophyletic Group
A
monophyletic taxon includes the most
recent common ancestor of a group and
all of its descendents.
Paraphyletic group
A
taxon is paraphyletic if it includes the
most recent common ancestor of a group
and some but not all of its descendents.
Polyphyletic grouping

A taxon is polyphyletic if it does not contain the
most recent common ancestor of all members of
the group.

This situation requires the group to have had
independent evolutionary origin of some
diagnostic feature. E.g. If you grouped birds,
butterflies and bats into a group you called
“WingedThings” it would be a polyphyletic group
because each group evolved wings separately.
Theories of taxonomy
 Both
traditional evolutionary taxonomy and
cladistics reject polyphyletic groups.
 They
both accept monophyletic groups,
but differ in their treatment of paraphyletic
groupings.
Traditional Evolutionary Taxonomy

TET uses two principles for designating taxa.



Common descent
Amount of adaptive evolutionary change
The second criterion leads to the idea that
groups may be designated as higher level taxa
because they represent a distinct “adaptive
zone” (Simpson) because they have undergone
adaptive change that fits them to a unique role
(e.g. penguins, humans).
Traditional Evolutionary Taxonomy
 Classification
 The
of anthropoid primates.
genera Gorilla, Pan (chimpanzee) and
Pongo (orang utan) are paraphyletically
grouped into family Pongidae and humans
(genus Homo) into family Hominidae even
though humans are phylogenetically closer
to Gorilla and Pan than either of those is to
Pongo.
Traditional Evolutionary Taxonomy
 Under
TET designation of family
Hominidae is because humans represent
a different grade of organization.
 Humans
are terrestrial, intelligent,
omnivores with advanced cultures.
 Members
of Pongidae are arboreal, less
intelligent, herbivores.
Traditional Evolutionary
Taxonomy
 In
a similar fashion “vertebrates” have
been historically distinguished from
“invertebrates” because the backbone,
development of the skull and other
features such as much greater size are
considered as making them substantially
different.
Cladistics
 Cladistics
emphasizes the criterion of
common descent. The cladistic approach
proposed by Willi Hennig in 1950.
 Under
cladistic rules all groups must be
monophyletic. Thus, cladists would group
the Pongidae and Hominidae into one
group the Hominidae.
Current taxonomy
 Current
taxonomy was developed using
evolutionary systematic approaches, but
has been extensively revised in part using
cladistic approaches.
 How
classification may finally be resolved
is unclear, but the issues of paraphyletic
groups and grades remain to be sorted
out.
Taxonomy for this semester
 For
this course we will base our
organization on the cladistic phylogeny of
Guillaume Lecointre and Herve Le
Guyader (2006) from their book “The Tree
of Life.”
 Bear
in mind that their classification is a
hypothesis about the evolutionary
relationships of groups and will be revised
in the future.
Placozoa
Demospongiae
Hexactinellida
Metazoa
Calcarea
Cnidaria
Ctenophora
Protostomia
Deuterostomia
Eutrochozoa: Rotifera, Acanthocephala,
Entoprocta,Platyhelminthes, Nemertea, Mollusca,
Sipuncula, Annelida
Lophotrochozoa
Lophophorata: Ectoprocta, Brachiopoda,
Phoronida
Protostomia
Ecdysozoa: Onychophora, Tardigrada,
Arthropoda, Nematoda, Nematomorpha,
Kinorhyncha, Loricifera, Priapulida
Cuticulata
Gastrotricha
Echinodermata
Deuterostomia
Hemichordata
Urochordata
Chordata
Cephalochordata
Craniata (includes the Vertebrata)